LMA CyTOF Core Resources

Cytoforum

The Cytoforum is the best place to connect with the greater CyTOF community on a variety of topics ranging from experimental design, instrument operation, data analysis and more. Search older posts, ask your questions, get information on publications, and answer questions in your area of expertise.

Protocols

Protocols for antibody conjugation, cell surface, viability, cytoplasmic targets, nuclear targets, signaling proteins and phosphoproteins can be found on Fluidigm's website by scrolling down to the CyTOF section. They can also be accessed when logged into the panel design tool website (see the panel design button above).

The Nolan Lab at Stanford has protocols available for stimulation, cell surface, methanol permeabilization and saponin permeabilization. They also provide protocols for validating and titrating antibodies, Max-Par antibody conjugation, and removal of carrier buffers in antibodies,

Data Analysis Tools and Information

Commercially available software can be used to analyze your CyTOF data. Cytobank, FlowJo and FCS Express will all allow for basic analysis such as bivariate plots, histogram overlays, heatmaps and dose response. Cytobank also offers user-friendly versions of ViSNE, SPADE, and Citrus for analyzing high dimensional data. You will need to download the most current version of FlowJo and FCS Express to accurately view your CyTOF data. Cytobank is also cloud-based so your data can be accessed from any computer, anywhere. FlowJo and Cytobank can also be accessed on the CyTOF and Flow Core Data Workstations

Free software designed for MatLab and R can be downloaded from Nolan Lab and Dana Pe'er Lab. Both sites also offer overviews and instructions for each type of analysis available. ACCENSE, a alternative tSNE algorithm is also available for download independently.

Normalization, concatenation, debarcoding, and FCS to TXT is available in the Fluidigm Helios software. This can be done in the core on the instrument computers or the CyTOF data workstation. A freestanding version is available for download online (PC only!)